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Transcript
Genetics and Resistance
New Gene for Bacterial Blight Resistance in Rice Located
on Chromosome 12 Identified from Minghui 63,
an Elite Restorer Line
Huilan Chen, Shiping Wang, and Qifa Zhang
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
Accepted for publication 28 February 2002.
ABSTRACT
Chen, H., Wang, S., and Zhang, Q. 2002. New gene for bacterial blight
resistance in rice located on chromosome 12 identified from Minghui 63,
an elite restorer line. Phytopathology 92:750-754.
Bacterial blight, caused by Xanthomonas oryzae pv. oryzae, is a serious disease of rice worldwide. A new dominant gene for bacterial blight
resistance in rice, Xa25(t), was identified from Minghui 63, a restorer
line for a number of rice hybrids that are widely cultivated in China. This
gene conferred resistance to Philippine race 9 (PXO339) of X. oryzae pv.
Bacterial blight, caused by Xanthomonas oryzae pv. oryzae, is
one of the most destructive diseases of rice worldwide. Numerous
major genes with resistance to various strains of X. oryzae pv.
oryzae have been identified, which have been named in a series
from Xa1 to Xa24 (9,10,12,25). More than 10 bacterial blight
resistance (R) genes are mapped on rice chromosomes 4 (Xa1,
Xa2, Xa12, and Xa14), 5 (xa5), 6 (Xa7), 8 (xa13), and 11 (Xa3,
Xa4, Xa10, Xa21, Xa22, and Xa23), with some of the genes being
allelic or tightly linked with each other (9,10,12,25). The chromosomal locations for the rest of the bacterial blight resistance genes
are still unknown.
More than 30 plant R genes have now been cloned. Most of the
cloned R genes encode 1 to 3 recognizable structural domains,
including leucine zipper (LZ), Toll-IL-1R homology region (TIR),
nucleotide-binding site (NBS), leucine-rich repeat (LRR), and
protein kinase (3). Four R genes, Xa21, Xa1, Pi-b, and Pi-ta, have
been isolated from rice. The bacterial blight resistance genes Xa21
and Xa1 encode the LRR-kinase protein and the NBS-LRR protein, respectively (16,22), and the blast resistance genes Pi-b and
Pi-ta encode NBS-LRR type proteins (1,19).
Minghui 63 is the male parent for a number of widely used
hybrids in rice production in China. It also is called a restorer line
because it restores the fertility of the F1 hybrid after crossing with
a male-sterile line. The major characteristics of the hybrids produced with Minghui 63 are high yield and wide adaptability,
which enable these hybrids to occupy more than 20% of the total
rice production area in China for the last 20 years. The wide
adaptability of these hybrids is due in part to the resistance of
Minghui 63 to bacterial blight, one of the most serious diseases of
rice in south China. Previous study indicated that Minghui 63
carries a dominant gene located on chromosome 11 for resistance
to a Chinese strain of X. oryzae pv. oryzae, JL691 (17). In a screen
of Minghui 63 to the Philippine isolates of X. oryzae pv. oryzae,
Corresponding author: S. Wang; E-mail address: [email protected]
Publication no. P-2002-0422-03R
© 2002 The American Phytopathological Society
750
PHYTOPATHOLOGY
oryzae in both seedling and adult stages. It was mapped to the centromeric region of chromosome 12, 2.5 cM from a disease resistance genehomologous sequence, NBS109, and 7.3 cM from a restriction fragment
length polymorphism marker, G1314. The genomic location of this gene
is similar to the previously identified blast resistance genes, Pi-ta and
Pi-ta2.
Additional keywords: mapping, R gene.
we found that this rice cultivar was also incompatible with strain
PXO339. This suggests that Minghui 63 may carry other bacterial
blight resistance genes responsible for its enduring resistance. The
objectives of this study were to determine if Minghui 63 carries
any unknown bacterial blight resistance gene or genes, and to
characterize them.
MATERIALS AND METHODS
Mapping population. A population of recombinant inbred lines
(RILs) of rice was used in this study. This population consisted of
241 lines developed by single-seed descendent from a cross between Zhenshan 97 (Oryza sativa subsp. indica) and Minghui 63
(O. sativa subsp. indica), the parents of Shanyou 63, the most
widely used hybrid in China. A molecular linkage map containing
221 loci and covering 1,790 cM was constructed with this population (20).
Pathogen inoculation and disease evaluation. For adult plant
inoculation, 11 seedlings of each RIL, Zhenshan 97, and Minghui
63 were planted in single rows spaced 26.4 cm apart. Plants were
spaced 16.5 cm apart in the row. At the booting stage (approximately 40 days after transplanting), 6 to 10 of the uppermost fully
expanded leaves of each plant were inoculated with the X. oryzae
pv. oryzae strains (Table 1) by the leaf clipping method (12). For
disease scoring, nine plants in the middle of each row were evaluated 3 weeks after inoculation. Four leaves with the longest lesion
from each of the nine plants were selected for analysis by measuring the lesion length and leaf length. The lesion area (percent) was
obtained by dividing the lesion length (centimeters) by the leaf
length.
For seedling stage inoculation, 10 seedlings each of Zhenshan
97 and Minghui 63 were planted in a greenhouse. The seedlings
were inoculated with the X. oryzae pv. oryzae strains at the three
to four-leaf stage by the same method used for the adult plants and
were scored for disease 2 weeks later (Table 1).
Data analysis. The lesion lengths of the plants after X. oryzae
pv. oryzae inoculation frequently were influenced by environment.
Therefore, the value at the valley of the distribution of lesion
length, instead of a fixed value, was used as the dividing point for
classifying plants into resistant and susceptible groups in a segregation population. The chromosomal location of the bacterial blight
resistance gene on the molecular linkage map was determined by
using Mapmaker/Exp 3.0 with an LOD threshold of 3.0 (13).
resistant (875) and susceptible (312) plants fit the expected 3:1
ratio (χ2 = 0.944, P > 0.25) if 10 cm in the apparent valley was
used as the dividing point (Fig. 2). These results suggested that
the resistance of Minghui 63 to PXO339 was controlled by a
single dominant gene.
Molecular mapping of the major gene conferring resistance
to PXO339. Using the lesion length of the RILs as the criterion,
the gene for resistance to PXO339 was mapped to the centromeric
region of chromosome 12, located between restriction fragment
length polymorphism (RFLP) markers R887 and G1314 (Fig. 3A).
No bacterial blight resistance gene previously has been mapped to
RESULTS
Resistance of experimental materials to X. oryzae pv.
oryzae strains. One of the parents of the RILs, Minghui 63, was
highly resistant to PXO339 and JL691 and moderately resistant
to PXO112 and T7147 at the adult plant stage; Minghui 63 also
was highly resistant to PXO339 and JL691 and moderately
resistant to PXO112 at the seedling stage (Table 1). The other
parent of the RILs, Zhenshan 97, was susceptible to all of the X.
oryzae pv. oryzae strains tested at both adult and seedling stages
(Table 1).
To identify whether the resistance of Minghui 63 to X. oryzae
pv. oryzae strain PXO339 was conferred by any previously identified R genes, five near-isogenic lines for bacterial blight resistance
(IRBB4, IRBB5, IRBB7, IRBB10, and IRBB14 carrying Xa4,
xa5, Xa7, Xa10, and Xa14, respectively), together with their recurrent susceptible parent, IR24, were examined for resistance to
PXO339 at the adult plant stage. These near-isogenic lines showed average lesion lengths of 4.4 cm (IRBB4), 11.4 cm (IRBB5),
0.7 cm (IRBB7), 12.8 cm (IRBB10), 10.6 cm (IRBB14), and
10.5 cm (IR24) 3 weeks after inoculation with PXO339, indicating that two genes, Xa4 and Xa7, located on chromosomes 11
and 6, respectively, were incompatible with PXO339.
The segregation patterns of the resistance to PXO339 in the
RIL and F2 populations. The distribution of lesion length for
PXO339 infection in the RIL population was bimodal with an
apparent valley at approximate 6 cm in the year 1999 (Fig. 1A).
Because of the difference in the leaf length between Zhenshan 97
and Minghui 63, the lesion area also was used as a criterion to
evaluate the resistance of the RILs to PXO339 infection. The lesion area showed a distribution pattern similar to that of the lesion
length (Fig. 1B), and the two measurements were highly correlated (r = 0.962). Using a lesion length of 6 cm as the dividing
point, the numbers of resistant and susceptible lines in the RIL
population were 115 and 126, respectively, and fit the expected
1:1 ratio (χ2 = 0.502, P > 0.25), indicating the involvement of a
major gene for resistance to PXO339.
We also investigated the resistance reaction of Minghui 63 to
PXO339 using an F2 population of 1,187 individuals from the
same cross in year 2000. The distribution of the lesion length in
the F2 population also appeared to be bimodal. The numbers of
Fig. 1. Distribution of A, lesion length and B, lesion area after PXO339
inoculation in the recombinant inbred line population derived from the cross
between Zhenshan 97 and Minghui 63.
TABLE 1. Lesion lengths (cm) of the parents of recombinant inbred lines after inoculation with Xanthomonas oryzae pv. oryzae
Booting stage
Strain
Philippine strains
PXO61 (race 1)
PXO86 (race 2)
PXO79 (race 3)
PXO71 (race 4)
PXO112 (race 5)
PXO99 (race 6)
PXO145 (race 7)
PXO280 (race 8)
PXO339 (race 9)
Chinese strains
JL691
LN44
Zhe173
Japanese strains
T7133
T7147
Seedling stage
Zhenshan 97
Minghui 63
Zhenshan 97
Minghui 63
19.9
22.7
21.2
20.2
8.9
22.3
21.0
17.5
20.6
14.3
14.7
21.3
13.3
6.3
28.1
16.1
21.0
0.9
14.5
16.2
11.8
11.9
10.2
…
…
7.9
7.5
16.1
14.4
11.8
13.7
5.3
…
…
8.7
1.6
22.0
20.2
15.7
1.0
7.5
9.4
8.9
…
14.3
0.7
…
9.6
20.1
15.8
8.5
6.1
26.8
11.2
14.1
10.7
Vol. 92, No. 7, 2002
751
To take a candidate gene approach to the Xa25(t) locus, two
clones from rice, NBS109 and NBS5, that were previously
mapped to this chromosomal region (M. A. Saghai Maroof, unpublished data) and contained sequences homologous to the NBS
domain of disease resistance genes, were used as probes to test
their cosegregation with Xa25(t). Only NBS109 detected polymorphism between the two parents by RFLP analysis and was located
at a distances of 2.5 cM from Xa25(t) and 0.5 cM from R887 (Fig.
3A). The new gene, therefore, is flanked by molecular markers
NBS109 and G1314 with an estimated genetic distance of 2.5 cM
from NBS109 and 7.3 cM from G1314. A rice population consisting of 172 F2 individuals derived from a cross between cv. Aijiao
Nante (O. sativa subsp. indica) and a common wild rice (O.
rufipogon), P16, was also used to map the two NBS sequences. A
molecular linkage map based on this F2 population contained 612
loci (21). Both NBS109 and NBS5 detected polymorphism between the parents of the F2 population and the two sequences were
closely linked in the centromeric region of chromosome 12 (Fig.
3B).
Resistant spectrum of Xa25(t). It is known that the gene in
Minghui 63 for resistance to JL691 is located on chromosome 11
(17). In order to separate the effects of Xa25(t) from the one on
chromosome 11, we determined the approximate location of the
resistance gene on chromosome 11 using the RIL population,
which was in the terminal region of the long arm of chromosome 11 flanked by RFLP markers L1044 and Y6855RA (Fig. 4).
Because several other genes for bacterial blight resistance
(e.g., Xa3, Xa4, Xa22, and Xa23) (12,14,23,25) also were located
in this region, its relationship with these genes remained to be
determined.
Five RILs were selected on the basis of molecular genotypes in
these two regions (Table 2). Two RILs (R4 and R128) had
Zhenshan 97 genotypes at the unnamed resistance locus on chromosome 11, thus carrying the susceptible allele of this locus, and
had Minghui 63 genotypes in Xa25(t) region, thus carrying the
resistant allele of this locus. The other three RILs (R19, R20, and
R202) had exactly the reverse genotypes in the two regions. The
five lines and their parents were inoculated with 11 X. oryzae pv.
this location; therefore, the gene against PXO339 in Minghui 63 is
a new R gene in the sense that no known gene for bacterial blight
resistance has been mapped to this chromosome. We tentatively
designate this new gene as Xa25(t).
Fig. 2. Distribution of lesion length after PXO339 inoculation of an F2 population derived from the cross between Zhenshan 97 and Minghui 63.
Fig. 3. The location of Xa25(t) gene and nucleotide-binding site (NBS)
sequences on the molecular linkage maps of chromosome 12. The maps were
based on the recombinant inbred line population from A, Zhenshan 97–
Minghui 63 and B, the F2 population from Aijiao Nante–P16. The solid
black box in map A represents the relative location of the centromeric region
according to the mapping information of Wang et al. (18).
Fig. 4. The location of a bacterial blight resistance gene against Xanthomonas oryzae pv. oryzae strain JL691 in chromosome 11. The solid box
indicates the chromosomal region containing the unnamed resistance gene.
TABLE 2. The genotypes of five selected recombinant inbred lines on the chromosomal regions containing bacterial blight resistance genesa
Markers across the region containing the unnamed R gene on chromosome 11
Rice line
R4
R128
R19
R20
R202
a
Y6854L
RM224
R1506
Y6855RA
R887
NBS109
G1314
Z
Z
M
M
Z
Z
Z
M
M
M
Z
Z
M
M
M
Z
Z
M
M
M
Z
Z
M
M
M
M
M
Z
Z
Z
M
M
Z
Z
Z
M
M
Z
Z
Z
Z = homozygous for Zhenshan 97 and M = homozygous for Minghui 63.
752
Markers across the Xa25(t) region
L1044
PHYTOPATHOLOGY
oryzae strains, including 7 Philippine strains (PXO61, PXO86,
PXO79, PXO71, PXO112, PXO280, and PXO339), 2 Chinese
strains (JL691 and ZJ173), and 2 Japanese strains (T7133 and
T7147) at seedling and booting stages in 2001.
At the seedling stage, RILs carrying Xa25(t) appeared to be
resistant to strain PXO339, whereas those carrying the unnamed R
gene on chromosome 11 were susceptible to PXO339 (data for
three of the strains are given in Table 3). All five RILs were resistant to strain JL691 but with the lesions two to three times as long
as that of Minghui 63, suggesting that the two genes enhanced
each other in the resistance of Minghui 63 to JL691 (Table 3). All
five RILs also showed partial resistance to PXO112, which is
approximately the same level of resistance as found in Minghui 63
(Table 3). Thus, the absence of either of the two genes did not influence the resistance to PXO112.
At booting stage, lines R4 and R128 still were resistant to
PXO339 but became susceptible to JL691 (Table 3). The other
three RILs were resistant only to JL691. These results suggest that
Xa25(t) was resistant to PXO339 at both seedling and adult
stages, and resistant to JL691 at the seedling stage but not the
adult stage. The results also indicated that the unnamed R gene on
chromosome 11 had no effect on the resistance to PXO339 at
either seedling or adult stage.
DISCUSSION
The present study identified a new dominant gene, Xa25(t), for
bacterial blight resistance in Minghui 63, a restorer line for a
number of widely used hybrids in rice production in China. The
new gene conferred resistance in Minghui 63 to the X. oryzae pv.
oryzae strain PXO339 at both seedling and adult stages. This gene
also partly contributed to the resistance of Minghui 63 to a
Chinese X. oryzae pv. oryzae strain, JL691, at seedling stage. The
resistance of the unnamed gene on chromosome 11 appeared to
affect only one X. oryzae pv. oryzae strain; therefore, it is reasonable to assume that Xa25(t) has made a major contribution to the
resistance of the hybrids in the last 2 decades.
A number of rice R genes previously were mapped to chromosome 12 and all of them conferred resistant to blast. Among these
genes, Pi-ta and Pi-ta2 have been identified as being allelic or
tightly linked with each other and located on the centromeric
region corresponding to the location of Xa25(t) determined in this
study (1,15). There also were a number of blast resistance genes,
including Pi-4a(t), Pi-4b(t), Pi-6(t), Pi-12(t), Pi-19, and Pi-20 (6–
8,24,26), that also were mapped to the centromeric region of
chromosome 12. A tightly linked cluster containing at least seven
blast resistant genes was mapped in the same region as Pi-ta and
TABLE 3. Lesion lengths (cm) of the five selected recombinant inbred lines
and the parents after Xanthomonas oryzae pv. oryzae inoculation in 2001
X. oryzae pv. oryzae strain
Rice line
Seedling stage
R4
R128
R19
R20
R202
Zhenshan 97
Minghui 63
Booting stage
R4
R128
R19
R20
R202
Minghui 63
Zhenshan 97
JL691
PXO339
PXO112
2.2
1.9
1.4
1.9
1.4
8.9
0.7
1.8
1.9
9.5
7.5
4.5
7.5
1.6
5.8
3.9
5.8
3.2
6.6
10.2
5.3
8.5
18.1
2.3
1.8
0.8
0.9
9.4
4.6
2.4
11.1
10.8
8.5
1.0
11.0
…
…
…
…
…
…
…
Pi-ta2 (2). These results suggest that there is at least one multiple
gene family for disease resistance in the centromeric region of
chromosome 12.
Pi-ta encodes the NBS-LRR type protein (1). The present study
also located two closely linked NBS sequences to the centromeric
region of chromosome 12. R proteins containing NBS motif also
have the LRR motif according to the structures of cloned R genes;
this suggests that there is at least one NBS-LRR type multiplegene family in the centromeric region of chromosome 12. Different copies of genes in the multiple-R-gene family or the alleles of
R loci are commonly the sources for the diversity of recognition
specificity in plant resistance to pathogen infection. The L locus
of flax contains a single gene of TIR-NBS-LRR type, and 11
alleles with different specificities of resistance to rust fungi have
been identified (5,11). The P and P2 genes against flax rust are
allelic or tightly linked in the locus containing the TIR-NBS-LRR
type multiple-gene family. The two genes encode proteins that differ by 10 amino acids (aa), but only 6 aa changes are sufficient to
alter P2 to the P resistant specificity (4). Therefore, the different
specificities of blast resistance identified in the loci of centromeric
region of rice chromosome 12 by previous studies may contribute
to the allelic or tightly linked copies of the genes in the multiple
gene family. There were two possibilities regarding the origin and
the identity of Xa25(t). One possibility is that the identified
Xa25(t) is a mutant in one of the blast resistance loci, thus being
allelic with one or more of the blast resistance genes. The other
possibility is that it is at a locus tightly linked to the abovementioned blast resistance loci. Resolving the two possibilities will
provide a good opportunity for studying recognition specificity of
resistance genes with bacterial blight and fungal blast.
ACKNOWLEDGMENTS
This study was supported in part by a grant from the National Natural
Science Foundation of China and a grant from the National Key Program
on Basic Research and Development of China (973). We thank M. A.
Saghai Maroof of Virginia Polytechnic Institute and State University for
providing rice NBS clones and the International Rice Research Institute
for the near-isogenic lines of bacterial blight resistance and the Philippine strains of X. oryzae pv. oryzae.
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